This invention relates to tandem mass spectrometry. In particular, although not exclusively, this invention relates to tandem mass spectrometry using an ion trap to analyze and select precursor ions and a time-of-flight (TOF) analyzer to analyze fragment ions.
Structural elucidation of ionized molecules is often carried out using a tandem mass spectrometer, where a particular precursor ion is selected at the first stage of analysis or in the first mass analyzer (MS-1), the precursor ions are subjected to fragmentation (e.g. in a collision cell), and the resulting fragment (product) ions are transported for analysis in the second stage or second mass analyzer (MS-2). The method can be extended to provide fragmentation of a selected fragment, and so on, with analysis of the resulting fragments for each generation. This is typically referred to an MSn spectrometry, with n indicating the number of steps of mass analysis and the number of generations of ions. Accordingly, MS2 corresponds to two stages of mass analysis with two generations of ions analyzed (precursor and products).
Relevant types of tandem mass spectrometers include:
1. Sequential in space:                a. Magnetic sector hybrids (4-sector, Mag-Trap, Mag-TOF, etc). See for example F. W. McLafferty; Ed. Tandem mass spectrometry; Wiley-Interscience: New York; 1983        b. Triple quadrupole (Q), wherein the second quadrupole is used as an RF-only collision cell (QqQ). See for example Hunt D F, Buko A M, Ballard J M, Shabanowitz J, and Giordani A B; Biomedical Mass Spectrometry, 8 (9) (1981) 397–408.        c. Q-TOF (a quadrupole analyzer followed by a TOF analyzer). See for example H. R. Morris, T. Paxton, A. Dell, J. Langhorne, M. Berg, R. S. Bordoli, J. Hoyes and R. H. Bateman; Rapid Comm. in Mass Spectrom; 10 (1996) 889–896; and I. Chernushevich and B. Thomson, U.S. Patent Application Publication Number 20020030159.        d. TOF-TOF (two sequential TOF analyzers with a collisional cell in between). See for example T. J. Comish and R. J. Cotter, U.S. Pat. No. 5,464,985 (1995)        
2. Sequential in time: ion traps such as Paul trap (see for example R. E. March and R. J. Hughes; Quadrupole Storage Mass Spectrometry, John Wiley, Chichester, 1989), Fourier Transform Ion Cyclotron Resonance (FT ICR—see for example A. G. Marshall and F. R. Verdum; Fourier transforms in NMR, Optical and Mass Spectrometry, Elsevier, Amsterdam, 1990) radial-ejection linear trap mass spectrometer (LTMS—see for example M. E. Bier and J. E. Syka; U.S. Pat. No. 5,420,425), and axial-ejection linear trap mass spectrometer (see, for example, J. Hager US-A-6,177,668).
3. Sequential in Time and Space:                a. 3D-TOF (See for example S. M. Michael, M. Chen and D. M. Lubman; Rev. Sci. Instrum. 63(10)(1992) 4277–4284 and E. Kawato, published as PCT/WO99/39368).        b. LT/FT-ICR (See for example M. E. Belov, E. N. Nikolaev, A. G. Anderson et al.; Anal Chem., 73 (2001) 253, and J. E. P. Syka, D. L. Bai, et al. Proc. 49th ASMS Conf. Mass Spectrom., Chicago, Ill., 2001).        c. LT/TOF (e.g., Analytica LT-TOF as in C. M. Whitehouse, T. Dresch and B. Andrien, U.S. Pat. No. 6,011,259) or Quadrupole-trap/TOF (J. W. Hager, U.S. Pat. No. 6,504,148).        
A number of non-sequential mass spectrometers suitable for tandem mass spectrometry have also been described (see for example J. T. Stults, C. G. Enke and J. F. Holland; Anal Chem., 55 (1983) 1323–1330 and R. Reinhold and A. V. Verentchikov; U.S. Pat. No. 6,483,109).
For example, U.S. Pat. No. 6,504,148 by J. W. Hager discloses a tandem mass spectrometer comprising a linear ion trap mass spectrometer, a trapping collision cell for ion fragmentation arranged axially, followed by a TOF mass analyzer.
PCT/WO01/15201 discloses a mass spectrometer comprising two or more ion traps and, optionally, a TOF mass analyzer, all arranged axially. The ion traps may function as collision cells and so the spectrometer is capable of MS/MS and MSn experiments.
Both of these spectrometers are standard in that they rely on axial ejection of ions from the ion trap to the collision cell and onwards to the time of flight analyzer. Both spectrometers also suffer from a problem that there is a conflict between speed of analysis (i.e. number of MS/MS experiments per second) and space-charge effects. To ensure sufficient numbers of fragmented ions are detected by the TOF mass analyzer to give sound experimental data, ever-increasing ion abundances must be stored upstream (particularly where more than one precursor ion is to be fragmented and analyzed). The need for high ion abundances upstream in the first analyzer is in conflict with the fact that the greater the ion abundance, the worse the resolution and accuracy of this analyzer because of space charge effects. For emerging high-throughput applications such as proteomics, it is important to provide unattainable yet speeds of analysis, on the order of hundreds of MS/MS spectra per second (as opposed to present limit of 5–15). This in its turn requires both efficient, space-charge tolerant utilisation of all incoming ions and fast, on the order of ms, analysis of each individual precursor m/z. Though time of flight analyzers on their own allow such speeds of analysis, all preceding parts of the system, namely ion trap and collision cell, should also match this so far unresolved challenge.